In this study, crystals of Z-DNA hexamer d(CGCGCG) complexed with MgCl2 and CaCl2 were obtained in the presence of high concentrations of alkaline earth salts (500 mM) using a temperature control technique, and their crystal structures were determined at 1.3 angstrom resolution. Mg2+ and Ca2+ cations in these structures tend to interact directly with phosphate groups of Z-DNA duplexes: however, they tend to form water-mediated interactions with Z-DNA in the presence of lower concentrations of alkaline earth salts. In these crystals, a DNA duplex was laid along its c-axis and interacted with its 6 neighboring DNA duplexes through coordination bonds of P-O-center dot center dot center dot(Mg2+ or Ca2+)(center dot center dot center dot)O-P. A symmetrical hexagonal Z-DNA duplex assembly model may explain DNA condensation caused by alkaline earth salts. These structures offer insights into the functions of alkaline earth cations essential to the structures and assembly of Z-DNA duplexes. (C) 2013 Elsevier Inc. All rights reserved.